Merge branch 'development' into stage

.github/workflows/docker-image-arm.yml

@@ -40,16 +40,16 @@ jobs:
         uses: docker/metadata-action@v4
         with:
           images: | 
-            agroportal/ontologies_api
-            ghcr.io/agroportal/ontoloportal_web_ui
+            agroportal/ontoportal_web_ui
+            ghcr.io/${{ github.repository }}
 
       - name: Build and push Docker image
         uses: docker/build-push-action@v4
         with:
           context: .
           platforms: linux/arm64
           build-args: |
-            RUBY_VERSION=2.7
+            RUBY_VERSION=2.7.8
           push: true
           tags: ${{ steps.meta.outputs.tags }}-${{ env.BRANCH_NAME }}-arm64
           labels: ${{ steps.meta.outputs.labels }}

.github/workflows/docker-image.yml

@@ -40,16 +40,16 @@ jobs:
         uses: docker/metadata-action@v4
         with:
           images: |
-            agroportal/ontoloportal_web_ui
-            ghcr.io/agroportal/ontoloportal_web_ui
+            agroportal/ontoportal_web_ui
+            ghcr.io/${{ github.repository }}
 
       - name: Build and push Docker image
         uses: docker/build-push-action@v4
         with:
           context: .
           platforms: linux/amd64
           build-args: |
-            RUBY_VERSION=2.7
+            RUBY_VERSION=2.7.8
           push: true
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}

.github/workflows/tests.yml

@@ -43,7 +43,7 @@ jobs:
           bundler-cache: true
 
       - name: Run OntoPortal API
-        run: bin/run_api -k ${{ env.REMOTE_API_KEY }} -r agroportal -t stage -s STY -u ${{ env.REMOTE_API_URL }}
+        run: bin/run_api -k ${{ env.REMOTE_API_KEY }} -r agroportal -t development -s STY -u ${{ env.REMOTE_API_URL }}
 
       # Add or replace database setup steps here
       - name: set up config file
@@ -55,8 +55,7 @@ jobs:
       # Add or replace test runners here
       - name: Run tests
         run:  COVERAGE=true RAILS_ENV=test bin/rails test -v
-      - name: Upload Code Coverage
-        uses: actions/upload-artifact@v2
-        with:
-          name: code-coverage
-          path: coverage/
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

Dockerfile

@@ -30,14 +30,14 @@ ENV RAILS_LOG_TO_STDOUT="1" \
     BUNDLE_WITHOUT="${BUNDLE_WITHOUT}"
 
 # fix for ruby v2.7.8 only
-RUN gem install uri -v 0.12.2 --no-document
+RUN gem install uri --no-document
 
 COPY Gemfile* .
 RUN bundle install
 
 RUN echo "--modules-folder /node_modules" > .yarnrc
 COPY package.json *yarn* ./
-RUN yarn install
+RUN yarn install && yarn build
 
 COPY . .
 

Gemfile

@@ -129,10 +129,12 @@ group :test do
   gem 'capybara'
   gem 'selenium-webdriver'
   gem 'simplecov', require: false
+  gem 'simplecov-cobertura' # for codecov.io
   #gem 'webdrivers'
 end
 
 
 gem "net-ftp", "~> 0.2.0", require: false
-gem "net-http"
+gem "net-http", "~> 0.3.2"
+
 

Gemfile.lock

@@ -279,7 +279,6 @@ GEM
       mime-types-data (~> 3.2015)
     mime-types-data (3.2023.1003)
     mini_mime (1.1.5)
-    mini_portile2 (2.8.5)
     minitest (5.20.0)
     msgpack (1.7.2)
     multi_json (1.15.0)
@@ -289,7 +288,7 @@ GEM
     net-ftp (0.2.0)
       net-protocol
       time
-    net-http (0.4.0)
+    net-http (0.3.2)
       uri
     net-imap (0.4.6)
       date
@@ -307,9 +306,6 @@ GEM
     newrelic_rpm (9.6.0)
       base64
     nio4r (2.6.1)
-    nokogiri (1.15.5)
-      mini_portile2 (~> 2.8.2)
-      racc (~> 1.4)
     nokogiri (1.15.5-x86_64-darwin)
       racc (~> 1.4)
     nokogiri (1.15.5-x86_64-linux)
@@ -480,6 +476,9 @@ GEM
       docile (~> 1.1)
       simplecov-html (~> 0.11)
       simplecov_json_formatter (~> 0.1)
+    simplecov-cobertura (2.1.0)
+      rexml
+      simplecov (~> 0.19)
     simplecov-html (0.12.3)
     simplecov_json_formatter (0.1.4)
     smart_properties (1.17.0)
@@ -503,7 +502,7 @@ GEM
     temple (0.10.3)
     terminal-table (3.0.2)
       unicode-display_width (>= 1.1.1, < 3)
-    terser (1.1.19)
+    terser (1.1.20)
       execjs (>= 0.3.0, < 3)
     thin (1.8.2)
       daemons (~> 1.0, >= 1.0.9)
@@ -548,7 +547,6 @@ GEM
     zeitwerk (2.6.12)
 
 PLATFORMS
-  ruby
   x86_64-darwin-23
   x86_64-linux
   x86_64-linux-musl
@@ -591,7 +589,7 @@ DEPENDENCIES
   multi_json
   mysql2
   net-ftp (~> 0.2.0)
-  net-http
+  net-http (~> 0.3.2)
   newrelic_rpm
   oj
   omniauth
@@ -618,6 +616,7 @@ DEPENDENCIES
   select2-rails
   selenium-webdriver
   simplecov
+  simplecov-cobertura
   sprockets-rails
   stackprof
   stimulus-rails

README.md

@@ -1,14 +1,39 @@
-### Configuration
+# Run ontologies_web_ui
+
+## Using OntoPortal UI utilities script
+### See help
+
+```bash 
+bin/ontoportal help
+```
+
 ```
-cp .env.sample .env 
+Usage: bin/ontoportal {dev|test|run|help} [--reset-cache] [--api-url API_URL] [--api-key API_KEY]
+  dev            : Start the Ontoportal Web UI development server.
+                  Example: bin/ontoportal dev --api-url http://localhost:9393 --api-key my_api_key
+                  Use --reset-cache to remove volumes: bin/ontoportal dev --reset-cache
+  test           : Run tests. Specify either a test file:line_number or  empty for 'all'.
+                  Example: $0 test test/integration/login_flows_test.rb:22
+  run            : Run a command in the Ontoportal Web UI Docker container.
+  help           : Show this help message.
+
+Description:
+  This script provides convenient commands for managing an Ontoportal Web UI
+  application using Docker Compose. It includes options for starting the development server,
+  running tests, and executing commands within the Ontoportal Web UI Docker container.
+
+Goals:
+  - Simplify common tasks related to Ontoportal Web UI development using Docker.
+  - Provide a consistent and easy-to-use interface for common actions.
 ```
 
+
 ### Run dev
 ```bash 
-bin/ontoportal dev 
+bin/ontoportal dev --api-url <an ontoportal api url> --api-key <my_api_key>
 ```
 
-### Run test with a local OntoPortal API  
+### Run test with a local OntoPortal API
 ```bash 
 bin/ontoportal test 
 ```

app/assets/stylesheets/bioportal.scss

@@ -49,6 +49,32 @@ body{
 
 }
 
+.disabled-link{
+  color: #888888 !important;
+  span{
+    opacity: 0.6;
+  }
+  a {
+    color: #888888 !important;
+  }
+  svg path{
+    fill: #888888 !important;
+  }
+}
+.text-truncate-scroll{
+  overflow: scroll;
+  white-space: nowrap;
+}
+
+
+.bg-warning-light{
+  background-color: var(--bg-warning-light-color) !important;
+}
+
+.bg-danger-light{
+  background-color: var(--bg-danger-light-color) !important;
+}
+
 @keyframes gradient {
   0% {
     background-position: 0% 50%;

app/assets/stylesheets/components/alert.scss

@@ -3,24 +3,26 @@
     align-items: center;
     padding: 20px;
     border-radius: 5px;
+
+
 }
+
 .alert-container.alert-info-type{
-    background-color: rgba(59, 130, 246, 0.1);
+    background-color:  var(--bg-info-light-color);
 }
 .alert-container.alert-warning-type {
-    background-color: rgba(234, 179, 8, 0.1);
+    background-color: var(--bg-warning-light-color);
 }
 .alert-container.alert-danger-type {
-    background-color: rgba(239, 68, 68, 0.1);
+    background-color: var(--bg-danger-light-color);
 }
 .alert-container.alert-success-type {
-    background-color: rgba(34, 197, 94, 0.1);
+    background-color: var(--bg-success-light-color);
 }
 
 
 
 
-
 .alert-message{
     font-size: 16px;
     margin: 0 10px;
@@ -43,8 +45,6 @@
 }
 
 
-
-
 .alert-icon svg{
     width: 25px;
     margin: 0 !important;

app/assets/stylesheets/theme-variables.scss.erb

@@ -33,7 +33,6 @@
             --primary-color: #5499a4;
             --hover-color: #6B96B7;
             --secondary-color: #ffc107;
-            --light-color: #F0F5F6;
             --admin-color: #145FF4;
             --light-color: #F1F6FA;
             --error-color: #EB4335;
@@ -44,6 +43,16 @@
 
 
 
+// common variables
+:root{
+    --container-max-width: 1248px;
+    --bg-info-light-color: rgba(59, 130, 246, 0.1);
+    --bg-danger-light-color: rgba(239, 68, 68, 0.1);
+    --bg-warning-light-color: rgba(234, 179, 8, 0.1);
+    --bg-success-light-color: rgba(34, 197, 94, 0.1);
+}
+
+
 
 
 

app/components/agent_search_input_component.rb

@@ -2,13 +2,13 @@
 
 class AgentSearchInputComponent < ViewComponent::Base
 
-  def initialize(id:, agent_type: nil, name_prefix: nil, parent_id: , edit_on_modal: false, deletable: false)
-    super
+  def initialize(id:, agent_type: nil, name_prefix: nil, parent_id: , show_affiliations: true, edit_on_modal: false, deletable: false)
     @id = id
     @agent_type = agent_type
     @name_prefix = name_prefix
     @parent_id = parent_id
     @edit_on_modal = edit_on_modal
+    @show_affiliations = show_affiliations
     @deletable = deletable
   end
 end

app/components/agent_search_input_component/agent_search_input_component.html.haml

@@ -1,7 +1,8 @@
-= render SearchInputComponent.new(name:'agent' + @id, ajax_url: "/ajax/agents?agent_type=#{@agent_type}&name=",
+= hidden_field_tag  "#{@name_prefix}[#{@id}]"
+= render SearchInputComponent.new(id: 'agent' + @id, name:'agent' + @id, ajax_url: "/ajax/agents?agent_type=#{@agent_type}&name=",
      item_base_url:"/agents/#{@id}?parent_id=#{@parent_id}&edit_on_modal=#{@edit_on_modal}&name_prefix=#{@name_prefix}&deletable=#{@deletable}&agent_id=", id_key: 'id',
      use_cache: false,
-     actions_links: {create_new_agent: {link: "/agents/new?name=&id=#{@id}&parent_id=#{@parent_id}&new_agent=false&type=#{@agent_type}&show_affiliations=false&edit_on_modal=#{@edit_on_modal}&name_prefix=#{@name_prefix}[#{@id}]", target:'_self'}}) do |s|
+     actions_links: {create_new_agent: {link: "/agents/new?name=&id=#{@id}&parent_id=#{@parent_id}&type=#{@agent_type}&show_affiliations=#{@show_affiliations}&deletable=#{@deletable}&edit_on_modal=#{@edit_on_modal}&name_prefix=#{@name_prefix}[#{@id}]", target:'_self'}}) do |s|
   - s.template do
     %a{href: "LINK", class: "search-content", 'data-turbo-frame': '_self'}
       %p.search-element.home-searched-ontology

app/components/chip_button_component/chip_button_component.html.haml

@@ -1,5 +1,6 @@
 - if @type == "static"
-    %span.chip_button_container{@html_options}
-        = @text || content
+  %span.chip_button_container{@html_options}
+    = @text || content
 - else
-    %a.chip_button_container_clickable{@html_options}= @text || content
+  %span.chip_button_container_clickable{@html_options}
+    = @text || content

app/components/input/select_component.rb

@@ -2,21 +2,23 @@
 
 class Input::SelectComponent < Input::InputFieldComponent
 
-  def initialize(id: nil, label: '', name:, value: [], selected: '', placeholder: '', error_message: '', helper_text: '', multiple: false, open_to_add_values: false, data: {}, tooltip: nil)
+  def initialize(id: nil, label: '', name:, value: [], selected: '', placeholder: '', error_message: '', helper_text: '', multiple: false, open_to_add_values: false, required: false,  data: {}, tooltip: nil)
     super(label: label, name: name, value: value, placeholder: placeholder, error_message: error_message,
           helper_text: helper_text, data: data)
     @values = value
     @selected = selected
     @open_to_add_values = open_to_add_values
     @multiple = multiple
     @id = id
+    @required = required
   end
 
   def call
     render Input::InputFieldComponent.new(name: @name, error_message: @error_message, helper_text: @helper_text, label: @label) do
       render SelectInputComponent.new(id: @id, name: @name, values: @values, selected: @selected,
-                                      placeholder: @placeholder,
-                                      multiple: @multiple, open_to_add_values: @open_to_add_values, data: @data)
+                                      placeholder: @placeholder, required: @required,
+                                      multiple: @multiple, open_to_add_values: @open_to_add_values,
+                                      data: @data)
     end
   end
 end

app/components/layout/horizontal_list_component.rb

@@ -9,7 +9,7 @@ def call
     content_tag(:div, class: 'd-flex flex-wrap align-items-center') do
       out = ''
       elements.each do |element|
-        out = out +  content_tag(:div, element, class: 'mr-1 mb-1 text-truncate overflow-hidden')
+        out = out +  content_tag(:div, element, class: 'mr-1 mb-1 text-truncate-scroll')
       end
       raw out
     end